use of def annotation

[cstoeckert]

Def is used to indicate country, city, province.
e.g., id: VEuGEO:0000011
name: Anguilla
alt_id: GADM:AIA
def: "Country" [GADM:AIA]
is_a: VEuGEO:0000002 ! North America
is_a: VEuGEO:0000004 ! Caribbean

Not clear this is correct - should discuss alternate ways to capture this information.

[cstoeckert]

We need to create a 'country', 'city', 'province' term - can base on GADM.
A country that is located in the Caribbean and North America.
Also need to use 'located in' rather than 'is-a'.
First step may need to be to generate classes from the terms provided in 'def'.

[bobular]

The "city/province/county/department" terms are now available in
https://github.com/VEuPathDB-ontology/VEuGEO/tree/main/src/ontology
GADM-English-ADM-types.txt

There are a lot of them! Note that for example "Province" is used at both GADM level 1 and 2.

At the same time, I modified the script (see documentation in the README in the directory linked above) to create a preliminary OBO file containing just the GADM-derived placename relationships.

Note that the VEuGEO:nnnnnn IDs in this file no longer correspond to the VBGEO:nnnnnn IDs but the GADM "alt_ids" (I know the use of alt_id is contentious) can be used to map VBGEO to VEuGEO when we are finished with VEuGEO.